The assemblies which define your content pipeline extension types, ie. a custom processor of some sort … need to be added as references to your mgcb, which can be done within the pipeline tool.
The assemblies added as references need to be built against MonoGame.Windows, specifically, to be loaded and used by the pipeline tool. If your content pipeline extension types are built against xna, or anything else, the pipeline tool will fail to load them and will not show your custom processors in the gui.